PurposeTo facilitate intraoperative localization of lung nodules, this study used model-based shape matching techniques to analyze the inter-subject three-dimensional surface deformation induced by pneumothorax. Methods: Contrast- enhanced computed tomography (CT) images of the left lungs of 11 live beagle dogs were acquired at two bronchial pressures (14 and 2 cm). To address shape matching problems for largely deformed lung images with pixel intensity shift, a complete Laplacian-based shape matching solution that optimizes the differential displacement field was introduced.ResultsExperiments were performed to confirm the methods’ registration accuracy using CT images of lungs. Shape similarity and target displacement errors in the registered models were improved compared with those from existing shape matching methods. Spatial displacement of the whole lung’s surface was visualized with an average error of within 5 mm.ConclusionThe proposed methods address problems with the matching of surfaces with large curvatures and deformations and achieved smaller registration errors than existing shape matching methods, even at the tip and ridge regions. The findings and inter-subject statistical representation are directly available for further research on pneumothorax deformation modeling.Electronic supplementary materialThe online version of this article (10.1007/s11548-019-02013-0) contains supplementary material, which is available to authorized users.